Marker-assisted backcrossing for a single gene

Marker-assisted backcrossing is the simplest form of MAS, in which the goal is to incorporate a major gene from an agronomically inferior source (the donor parent) into an elite cultivar or breeding line (the recurrent parent). The desired outcome is a line containing only the major gene from the donor parent, with the recurrent parent genotype present everywhere else in the genome. Two types of selection are recognized (Hospital, 2003):

  • Foreground selection, in which the breeder selects plants having the marker allele of the donor parent at the target locus. The objective is to maintain the target locus in a heterozygous state (one donor allele and one recurrent parent allele) until the final backcross is completed. Then, the selected plants are self-pollinated and progeny plants identified that are homozygous for the donor allele (Fig. 8).
  • Background selection, in which the breeder selects for recurrent parent marker alleles in all genomic regions except the target locus, and the target locus is selected based on phenotype. Background selection is important in order to eliminate potentially deleterious genes introduced from the donor. So-called ' linkage drag ', the inheritance of unwanted donor alleles in the same genomic region as the target locus, is difficult to overcome with conventional backcrossing, but can be addressed efficiently with the use of markers.

In practice, both foreground and background selection are often conducted in the same backcross program, either simultaneously or sequentially. An example of the combined use of foreground and background selection is shown in Fig. 8. 

Figure 8. Scheme for marker-assisted backcrossing of a single gene into an elite, recurrent parent line.

The efficiency of marker-assisted backcrossing depends on a number of factors, including the population size of each backcross generation, distance of markers from the target locus, and number of background markers used. Data from Hospital (2003) show faster recovery of the recurrent parent genome with MAS compared to conventional backcrossing when foreground and background selection are combined (Table 1). The recurrent parent genome is recovered more slowly on the chromosome carrying the target locus than on other chromosomes because of the difficulty in breaking  linkage with the target donor allele. Methods for optimizing sample sizes and selection strategies in marker-assisted selection are discussed by Bonnett et al. (2005), Frisch and Melchinger (2001), and Frisch et al. (1999a,b).

Table 1. Expected results of a typical marker-assisted backcrossing program, based on simulations of 1000 replicates (Hospital, 2003). In each backcross generation, heterozygotes were selected at the target locus. Recurrent parent alleles were selected at markers flanking the target locus (2 cM on either side) and at three markers on each non-target chromosome.


    % homozygosity of recurrent parent alleles at selected markers recurrent parent genome
Backcross generation Number of individuals Chromosome with target locus All other chromosomes Marker-assisted backcross Conventional backcross
BC1 70 38.4 60.6 79.0 75.0


100 73.6 87.4 92.2 87.5
BC3 150 93.0 98.8 98.0 93.7
BC4 300 100.0 100.0 99.0 96.9


  • A common application of marker-assisted backcrossing has been the introgression of transgenes into an adapted variety or line (e.g., introgression of the Bt insect resistance transgene into different maize genetic backgrounds). Often the target gene can be detected phenotypically, and markers are used to select for the recurrent parent genome. The technique has reportedly accelerated the recovery of the recipient genome by about two backcross generations (Hospital, 2003).
  • In Australia, a marker linked (0.7 cM) to the Yd2 gene for resistance to barley yellow dwarf virus was successfully used to select for resistance in a barley backcross breeding scheme (Jefferies et al., 2003). Field test data showed that BC2 F2-derived lines containing the linked marker had fewer leaf symptoms and higher grain yield when infected by the virus compared to lines lacking the marker.
  • Soybean yields were increased by using marker-assisted backcrossing to introgress a yield QTL from a wild accession into commercial genetic backgrounds (Concibido et al., 2003). Although the yield enhancement was observed in only two of six genetic backgrounds, the study demonstrates the potential of incorporating wild alleles with the assistance of markers.